ACELab wiki

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==== Software Listing ====

=== researchers list ===

  * Anaconda v4.2 for Python 2.7 (https://www.continuum.io/downloads)
  * AFNI
  * ANTs (http://stnava.github.io/ANTs/)
  * BEaST
  * BigBrain on line (https://bigbrain.loris.ca/main.php)
  * BrainSuite16a1 (http://brainsuite.org/)
  * BrainView
  * Caret
  * CIVET
  * Display
  * Deformation fields (mcvaneede)
  * Eigen v3.2 stable (http://eigen.tuxfamily.org/index.php?title=Main_Page)
  * FSL5.0 (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)
  * FreeSurfer v5.3 (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)
  * HCP Workbench (https://www.humanconnectome.org/software/get-connectome-workbench.html)
  * MATLAB Compiler Runtime R2015b (https://www.mathworks.com/products/compiler/mcr/)
  * Matlab based imaging tools
    * brainstorm3[[https://github.com/brainstorm-tools/brainstorm3]]
    * eeglab [[https://sccn.ucsd.edu/wiki/How_to_download_EEGLAB]]
    * fmristat [[http://www.math.mcgill.ca/keith/fmristat/]]
    * surfstat [[http://www.math.mcgill.ca/keith/surfstat/]]
    * niak ( https://www.nitrc.org/projects/niak/ )
    * spm8 [[http://www.fil.ion.ucl.ac.uk/spm/software/spm8/]]
    * spm12 [[http://www.fil.ion.ucl.ac.uk/spm/software/spm12/]]
  * MINC 1 + 2
  * Minc Tools / Display
    * pymin
  * MRICron tools (http://people.cas.sc.edu/rorden/mricron/install.html)
  * mri tutorials
  * Mrtrix3 (http://mrtrix.readthedocs.io/en/latest/installation/linux_install.html)
  * neurosynth
  * openmp
  * RMINC [[https://github.com/Mouse-Imaging-Centre/RMINC]]
  * SPM
  * JEMRIS (http://www.jemris.org/)

=== Neurodebian Packages ===

  * FSL
  * AFNI
  * pyMVPA
  * nibabel
  * mricron
  * psychtoolbox
  * odds and ends, converters, viewers and so on.


=== Utilities ===

  * apticron
  * Anaconda, miniconda and conda
  * FileZilla (https://filezilla-project.org/)
  * ethtool
  * GCC version to 4.8 if possible (https://gcc.gnu.org/gcc-4.8/)
  * GIMP
  * InkScape
  * OpenOffice
  * Perl
  * Python
    * cffi
    * cryptography
    * cython
    * enum34
    * idna
    * imagemagic
    * ipaddress
    * numpy
    * pip
    * pyasn1
    * pycosat
    * pycparser
    * pycrypto
    * pygobject
    * pyminc
    * pyOpenSSL
    * python-apt
    * scipy
    * scour
    * six
    * unity-lens-photos
  * R
  * Rminc
  * Slack
  * SublimeText
  * SurfStat
  * unattended-upgrades
  * Vim
  * VirtualBox
  * zlib (http://www.zlib.net/)

=== BrainVISA Anatomist ===

This software has not been tested by our IT Team. Feedback from our research team on this software would be appreciated.

== Description ==

BrainVISA Anatomist is a Neuroimaging software platform for mass data analysis

  * Morphologist: brain segmentation and sulcal morphometry
  * Processing tools and toolboxes
  * Interactive 3D neuroimaging data visualization
  * Software and data organization

== Resources ==

  * [[http://brainvisa.info/web/index.html | BrainVISA Homepage ]]
  * [[http://brainvisa.info/web/download.html | BrainVISA Downloads]]
  * [[http://brainvisa.info/web/download/go.php?url=http://brainvisa.info/packages/4.5.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.15-online.md5 | BrainVISA md5sums]]

=== MINC Tool Kit ===

This toolkit contains most of the commonly used minc tools in one precompiled 32 and 64bit binary packages of Debian, Ubuntu, RedHat and Mac OS X. It includes most of the standard minc tools, Display, Register and a basic image processing pipeline based on the one developed for NIHPD project (standard_pipeline.pl) Everything is currently installed in /opt/minc , to avoid conflict with standard /usr/local/bic location.

  * [[http://bic-mni.github.io/]]
  * [[http://bic-mni.github.io/#version-10081008-currently-stable]]

== MINC Metaproject

Metaproject uniting all the available minc tools

* [[https://github.com/BIC-MNI/minc-toolkit]]


== MINC References

* [[https://en.wikibooks.org/wiki/MINC]]

- Minc viewers such as:
  * Display
  * Register
  * BrainView [[https://github.com/sghanavati/brain-view2]]
  * ModelGui (Andrew Reid's)

=== SGE ===

Some form of a batch, SGE system that allows you to take advantage of parallel processing capabilities of CIVET/FSL tools

=== Python Scripts ===

== Pydpiper ==

a flexible toolkit for constructing novel registration pipelines

Miriam Friedel,Matthijs C. van Eede,M. Mallar Chakravarty,Jason P. Lerch

  * [[https://github.com/Mouse-Imaging-Centre/pydpiper]] < Preferred?
  * [[http://www.mouseimaging.ca/]]
  * [[https://github.com/bcdarwin/pydpiper]]
  * [[https://github.com/psteadman/pydpiper]]
  * [[https://github.com/pipitone/cv]]
  * mallar.chakravarty@douglas.mcgill.ca

=== Development, Programming and Scripting ===

  * adacity
  * build-essential
  * C
  * cmake
  * filezilla
  * GNC Make
  * gparted
  * latex
  * pbzip, pigz, rar, p7zip-full
  * pdftk, qpdf
  * Perl
  * Python
  * imagemagick
  * R
  * renameutils
  * scribus
  * sox
  * sshfs
  * tree
  * vim
  * Virtualbox
  * watch

=== RMINC ===

Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Jim Nikelski and others

* [[https://github.com/Mouse-Imaging-Centre/RMINC|RMINC]]


=== Matlab ===

(latest available version)

  * [[http://www.math.mcgill.ca/keith/fmristat/|fMRIstat]]
  * [[http://www.math.mcgill.ca/keith/surfstat/|Surfstat]]
  * [[http://www.fil.ion.ucl.ac.uk/spm/|Statistical Parametric Mapping (SPM) latest version]]
  * [[https://www.nitrc.org/projects/niak/ |NeuroImaging Analysis Kit (NIAK) latest version]]
  * Brainstorm and BESA (wish list)
  * CONN
  * GIFT

=== FreeSurfer ===

* latest version
* [[http://www.freesurfer.net/|freesurfer.net]]

=== FSL tools ===

* [[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL|FMRIB Software Library (FSL)]]
* Latest version, as per their website

=== C-PAC ===

* [[http://fcp-indi.github.io/|Configurable Pipeline for the Analysis of Connectomes (C-PAC)]]

=== itk-SNAP ===

ITK-SNAP is a software application used to segment structures in 3D medical images.

* [[http://www.itksnap.org/pmwiki/pmwiki.php|itk-SNAP]]
* [[http://www.itksnap.org/pmwiki/pmwiki.php?n=SourceCode.SourceCode]]

=== Human Connectome Project (HCP) connectome workbench ===

Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.

* [[http://www.humanconnectome.org/software/connectome-workbench.html|HCP connectome workbench]]

=== SOLAR (Sequential Oligogenic Linkage Analysis Routines) ===

* Genetics
* See "Solar Eclipse Imaging Genetics tools"

SOLAR is a flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening.

== Solar Eclipse Imaging Genetics tools ==

SOLAR-Eclipse is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening.

* [[http://solar-eclipse-genetics.org/|SOLAR-Eclipse: An Imaging Genetics Analyses Software]]
* [[http://solar-eclipse-genetics.org/downloads.html|Linux Solar Eclipse Downloads]]

== Other LINKAGE ANALYSIS PROGRAMS ==

University of Alabama at Birmingham - Section on Statistical Genetics (SSG) - Listong of [[http://www.soph.uab.edu/ssg/linkage/linkageanalysis|linkage analysis ptograms]]
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